SBML Level 3: an extensible format for the exchange and reuse of biological models

SM Keating, D Waltemath, M König, F Zhang… - Molecular systems …, 2020‏ - embopress.org
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …

Towards reproducible computational drug discovery

N Schaduangrat, S Lampa, S Simeon… - Journal of …, 2020‏ - Springer
The reproducibility of experiments has been a long standing impediment for further scientific
progress. Computational methods have been instrumental in drug discovery efforts owing to …

[ספר][B] Reproducibility and replicability in science

National Academies of Sciences, Medicine, Policy… - 2019‏ - books.google.com
One of the pathways by which the scientific community confirms the validity of a new
scientific discovery is by repeating the research that produced it. When a scientific effort fails …

Unraveling the molecular mechanism of action of empagliflozin in heart failure with reduced ejection fraction with or without diabetes

O Iborra-Egea, E Santiago-Vacas, SR Yurista… - JACC: Basic to …, 2019‏ - jacc.org
The mechanism of action of empagliflozin in heart failure with reduced ejection fraction
(HFrEF) was deciphered using deep learning in silico analyses together with in vivo …

Mechanisms of action of sacubitril/valsartan on cardiac remodeling: a systems biology approach

O Iborra-Egea, C Gálvez-Montón, S Roura… - NPJ systems biology …, 2017‏ - nature.com
Sacubitril/Valsartan, proved superiority over other conventional heart failure management
treatments, but its mechanisms of action remains obscure. In this study, we sought to explore …

Parameter estimation and uncertainty quantification for systems biology models

ED Mitra, WS Hlavacek - Current opinion in systems biology, 2019‏ - Elsevier
Mathematical models can provide quantitative insights into immunoreceptor signaling, and
other biological processes, but require parameterization and uncertainty quantification …

Harmonizing semantic annotations for computational models in biology

ML Neal, M König, D Nickerson, G Mısırlı… - Briefings in …, 2019‏ - academic.oup.com
Life science researchers use computational models to articulate and test hypotheses about
the behavior of biological systems. Semantic annotation is a critical component for …

Microbiome modeling: a beginner's guide

E Lange, L Kranert, J Krüger, D Benndorf… - Frontiers in …, 2024‏ - frontiersin.org
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in
human health, environmental processes, and biotechnological applications and interact with …

[HTML][HTML] Use of nonintrusive sensor-based information and communication technology for real-world evidence for clinical trials in dementia

S Teipel, A König, J Hoey, J Kaye, F Krüger… - Alzheimer's & …, 2018‏ - Elsevier
Cognitive function is an important end point of treatments in dementia clinical trials.
Measuring cognitive function by standardized tests, however, is biased toward highly …

Tellurium notebooks—an environment for reproducible dynamical modeling in systems biology

JK Medley, K Choi, M König, L Smith, S Gu… - PLoS computational …, 2018‏ - journals.plos.org
The considerable difficulty encountered in reproducing the results of published dynamical
models limits validation, exploration and reuse of this increasingly large biomedical …